I'd be interested in testing prototypes. I really like my current yeast transformation protocol because I find it easy enough, but I'd be very willing to test it out with E coli.

On Sunday, May 1, 2016 at 3:56:48 AM UTC, John Griessen wrote:

On 04/30/2016 09:29 AM, William Beeson wrote: > I will test transformations on E.coli and Neurospora crassa. I've had interest in a low cost electroporator for months. I think > the path to validation would be to show effectiveness with E. coli first (a much easier organism to transform). Then transition > to fungal cells which have much lower transformation efficiency. If you have the hardware expertise to build a device with > pre-programmed settings (say an E. coli and a fungal cells setting) I can do the lab work and prepare a data package for the product. > > -Will > > On Saturday, April 30, 2016 at 9:54:35 AM UTC-4, John Griessen wrote: > > On 04/29/2016 07:33 PM, William Beeson wrote: > > If anyone has ideas for how to get this to work well please post or share the ideas. The amount of electrical engineering > > involved in this is beyond my skill level.

How fast are you wanting this? I'm in the middle of another project. Anyone else interested in early testing of prototypes? These will be "junk prototypes". Similar to DIY art assemblages, but a little neater, and documented so a product could be made from them by a few revision iterations.

I'd be interesting in testing prototypes. I really like my current yeast transformation protocol because I find it easy enough, but I'd be very willing to test it out with E coli.

-Keoni

On Sunday, May 1, 2016 at 3:56:48 AM UTC, John Griessen wrote:

On 04/30/2016 09:29 AM, William Beeson wrote: > I will test transformations on E.coli and Neurospora crassa. I've had interest in a low cost electroporator for months. I think > the path to validation would be to show effectiveness with E. coli first (a much easier organism to transform). Then transition > to fungal cells which have much lower transformation efficiency. If you have the hardware expertise to build a device with > pre-programmed settings (say an E. coli and a fungal cells setting) I can do the lab work and prepare a data package for the product. > > -Will > > On Saturday, April 30, 2016 at 9:54:35 AM UTC-4, John Griessen wrote: > > On 04/29/2016 07:33 PM, William Beeson wrote: > > If anyone has ideas for how to get this to work well please post or share the ideas. The amount of electrical engineering > > involved in this is beyond my skill level.

How fast are you wanting this? I'm in the middle of another project. Anyone else interested in early testing of prototypes? These will be "junk prototypes". Similar to DIY art assemblages, but a little neater, and documented so a product could be made from them by a few revision iterations.

On 04/30/2016 09:29 AM, William Beeson wrote:
> I will test transformations on E.coli and Neurospora crassa. I've had interest in a low cost electroporator for months. I think
> the path to validation would be to show effectiveness with E. coli first (a much easier organism to transform). Then transition
> to fungal cells which have much lower transformation efficiency. If you have the hardware expertise to build a device with
> pre-programmed settings (say an E. coli and a fungal cells setting) I can do the lab work and prepare a data package for the product.
>
> -Will
>
> On Saturday, April 30, 2016 at 9:54:35 AM UTC-4, John Griessen wrote:
>
> On 04/29/2016 07:33 PM, William Beeson wrote:
> > If anyone has ideas for how to get this to work well please post or share the ideas. The amount of electrical engineering
> > involved in this is beyond my skill level.

How fast are you wanting this? I'm in the middle of another project.
Anyone else interested in early testing of prototypes? These will be "junk prototypes".
Similar to DIY art assemblages, but a little neater, and documented so a product
could be made from them by a few revision iterations.

It would be helpful if people created original content. A rewriting of the press release without adding a single iota of new information is less than helpful- and trying to ad-hominem critique me with such a reposting is trolling.

If you don't like my math, critique my math with better math. I've spotted at least one glaring error in my own post since I posted it- it's a thought in progress.

On Apr 29, 2016 10:48 PM, "BraveScience" <bravescience@gmail.com> wrote: > > Not all people have the knowledge, time, equipment and skills to isolate mycelium through clonal reproduction.

That is what the internet/books and friends/mentors at for.

> Giving them the chance to receive and use ready-to-use material doesn't sound a crazy ripoff but a good opportunity to start correctly. > > Moreover have you ever tried to isolate tissue from mushroom cap?

Yes, you pressure-cook some agar, get a few pressure-cooked knives/razors/scalpels, then wipe a mushroom with alcohol and maybe dip it in a bleach + sterile water solution, rinse well with sterile water, then shave layers off the mushroom, for each cut alcohol dipping and flame sterilizing the cutting tool. If it it really dirty, switch cutting tools. When you get a nice clean chunk exposed, place onto agar. Leave in kitchen cabinet for a few days and you will see mycelium, after a few months untouched it is not uncommon to get a small micro/mini mushroom.

> Much easier to have some already growing mothefucking thick piece of mycelium.

If you can't handle what I described above, there's probably not too much more someone would be able to do with a plate of mycelium, other than look at it die or possibly fruit. But I guess maybe there's a demand quickly available generic mycelium... I've never seen it sold like that before anywhere, so hard to imagine a use case.

I will test transformations on E.coli and Neurospora crassa. I've had interest in a low cost electroporator for months. I think the path to validation would be to show effectiveness with E. coli first (a much easier organism to transform). Then transition to fungal cells which have much lower transformation efficiency. If you have the hardware expertise to build a device with pre-programmed settings (say an E. coli and a fungal cells setting) I can do the lab work and prepare a data package for the product.

-Will

On Saturday, April 30, 2016 at 9:54:35 AM UTC-4, John Griessen wrote:

On 04/29/2016 07:33 PM, William Beeson wrote: > If anyone has ideas for how to get this to work well please post or share the ideas. The amount of electrical engineering > involved in this is beyond my skill level.

Will you commit to some testing? Maybe 4 times on the same filamentous fungal cells? Over weeks with little test circuit boards in the mail?

You're only interested in having this yesterday, so as soon as it works for you, the testing stops? If it doesn't get going in a week, you're out?

On 04/29/2016 07:33 PM, William Beeson wrote:
> If anyone has ideas for how to get this to work well please post or share the ideas. The amount of electrical engineering
> involved in this is beyond my skill level.

Will you commit to some testing? Maybe 4 times on the same filamentous fungal cells? Over weeks with little
test circuit boards in the mail?

You're only interested in having this yesterday, so as soon as it works for you, the testing stops?
If it doesn't get going in a week, you're out?

As you may have figured by the name of the shop and the product descriptions, the store is not really aiming at proficient microbiologists.

The hundreds of customers we had at our pop-up stores so far generally found it totally awesome to buy a microbe. Don't forget that most people have never seen something like that before.

We welcome all suggestions to make the store better, and more affordable. The best way to do it is to apply for the internship and help make it happen!

And don't worry, 30 euro might sound much, opening up a shop in the center of a popular shopping area of a capital city is expensive too. We will remain a non-profit organisation what ever happens anyway.

On Saturday, 30 April 2016 07:48:47 UTC+2, BraveScience wrote:

Not all people have the knowledge, time, equipment and skills to isolate mycelium through clonal reproduction.

Giving them the chance to receive and use ready-to-use material doesn't sound a crazy ripoff but a good opportunity to start correctly.

Moreover have you ever tried to isolate tissue from mushroom cap?Much easier to have some already growing mothefucking thick piece of mycelium.

I am very interested in this topic. To transform filamentous fungi it is most practical to use electroporation. There are very few protocols that are established for chemical transformation. If anyone has ideas for how to get this to work well please post or share the ideas. The amount of electrical engineering involved in this is beyond my skill level.

> It'd also be simple enough to add measurement of the discharge curve using a > voltage divider and the built in ADC of an atmega chip. > > Add an ESP8266 and you'd be able to connect via wifi+web to download and > view the conductance measurement and discharge graph for use in your > scientific article.

We had an awesome and unexpected evening last night exploring a pre-release version of Microsoft's HoloLens at Open Science Network here in Vancouver. I think this was the first public demo of the HoloLens in Vancouver outside of Alex Kipman's talk at the TED conference. It was totally last minute and the VR Roundtable group at UBC join us to get first hand exposure to the device. Even they haven't seen the HoloLens outside of the web. You can view some photos I took during the evening on our Facebook page.

Having access got me thinking about how the HoloLens can be used for protein structure analysis. Can you imaging walking through a field of protein structures imported from PDB and introspecting how different molecules interact in 3D? Can we build a 3D rendering of the inside of a cell, at least in part? Maybe follow a signalling event as it traverses from the cell surface to the nucleus. Imagine that!

Microsoft's HoloStudio app allows one to import standard STL 3D model files used for 3D printing. The awesome free VMD molecular modelling app allows us to import the publicly available protein structures and, critically, to export 3D structures as STL files. Some of you may have exposure to the traditional publicly available 3D protein modelling tools but it is a huge difference to be able to see a 3D hologram that you can interact with. Eventually I can envisage gestural commands that allow one to modify the amino acid sequence and see how that plays out in the 3D context. Then maybe we can sync those changes to gene synthesis companies to have the DNA for real world work. I love this blue sky stuff!

What would you do if you could build a room full of protein structures? How do you see this tech evolving?

On 04/29/2016 02:23 PM, Nathan McCorkle wrote:
> Now thinking back to those discussions, there was a lot of concern
> with isolation. Would a wireless microcontroller obviate most/all
> concerns? Obviously isolation would still be good to protect the
> microcontroller... but assuming isolation development time cost more
> than a few $2 replacement ESP8266... well, does that assumption hold
> true?

The isolation that is needed is for safety, not economy, so no you can't skip it
and ship a product and not get bad karma, sued, end up way worse off than Willie Nelson
when his financial manager set him up with "tax shelters"...etc.

Anyone on this list interested in doing some of the leg work with me?
for a product with an oshwa.org pedigree as a kit, and same thing assembled and ETL tested
for North America/Europe lab equipment level of safety. For lab equipment your lawsuit
for product harm damages fails if you stick your tongue in it, but not for household stuff
'where babies rule'.

I have some organisms I would like to transform, and frankly, electroporation just works better. I would love to use an open source one, but that isn't happening very soon, so I have been considering for a while getting a used one off ebay. Does anyone have experience with a good pulse chamber + power supply combo? I would like to know what has been worked on (like perhaps the invitrogen electroporator ii) before I commit to a purchase.

Now thinking back to those discussions, there was a lot of concern
with isolation. Would a wireless microcontroller obviate most/all
concerns? Obviously isolation would still be good to protect the
microcontroller... but assuming isolation development time cost more
than a few $2 replacement ESP8266... well, does that assumption hold
true?

On Fri, Apr 29, 2016 at 9:54 AM, John Griessen <john@industromatic.com> wrote:
> On 04/28/2016 02:00 AM, Patrik D'haeseleer wrote:
>> Given how dirt cheap flyback transformers and other high voltage gear are
>> on my favorite online discount site
>> <http://www.goldmine-elec-products.com/products.asp?dept=1480>, perhaps
>> that might be a better way to go.
>>
>
> I have a back burner project to develop that. There are so few asking for it
> though, so I work on another project
> to generate income to have enough momentum to develop anything at all first.
>
> On 04/28/2016 03:53 AM, Marc Juul wrote:
>> Add an ESP8266 and you'd be able to connect via wifi+web to download and
>> view the conductance measurement and discharge graph for
>> use in your scientific article.
>>
>
> I'll be making a multi pulser flyback version so it can stretch a pulse,
> (with many peaks), out to 5ms or cook for 300 ms
> if desired. And then the power flow and impedance can be adjusted for
> different conductivity test cells. I'm a backer of
> the micropython on esp8266 and could easily use that one as a controller for
> this project. Are you going to commit time, and
> will you license it open hardware compatible?
>
> On 04/28/2016 03:12 PM, Nathan McCorkle wrote:
>> Is electroporation preferable? From the first time I used it, my first
>> summer internship, I was hooked. I thought "screw chemical
>> transformation" for the, in my opinion, more elegant, tuneable,
>> eco-friendly/greener-chemistry, faster, wider species coverage (you
>> just vary the pulse shape/voltage, maybe the salt content of the
>> buffer)... and higher efficiency to boot.
>>
>> Why isn't it more prominent? Because no one has made a cheaper or
>> open-source version yet.
>
> OK, so will you help me promote it with twitter, instagram, snap chat videos
> when the time comes?
> Who to sell to besides DIYers?
>
> There were some discussions I kept "best of" emails from before 2014 when my
> list server crashed
> without a backup I can find anymore. We were talking with a retired Oak
> Ridge nuclear engineer
> developing RF induction heaters using a car induction coil. It's all a
> little heavy and expensive compared
> to the flyback parts used in laser printers -- I have a box full of those to
> test with...
>
> The list has been up again since just after that crash if anyone wants to
> use it.
> http://lists.cibolo.us/mailman/listinfo/open_electroporator> I think here on diybio@googlegroups.com is good for worthwhile
> milestones, and there have not really been any. Not much was lost from that
> crash.
> For saving old crusty details, there is anew list serve besides googlegroups
> by an original Yahoo.com
> businessman called groups.io -- it will have ads.
>
> John Griessen
>
> --
> -- You received this message because you are subscribed to the Google Groups
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> To unsubscribe from this group, send email to
> diybio+unsubscribe@googlegroups.com. For more options, visit this group at
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> To view this discussion on the web visit
> https://groups.google.com/d/msgid/diybio/572391D6.5070209%40industromatic.com.
> For more options, visit https://groups.google.com/d/optout.

I have a back burner project to develop that. There are so few asking for it though, so I work on another project
to generate income to have enough momentum to develop anything at all first.

On 04/28/2016 03:53 AM, Marc Juul wrote:
> Add an ESP8266 and you'd be able to connect via wifi+web to download and view the conductance measurement and discharge graph for
> use in your scientific article.
>

I'll be making a multi pulser flyback version so it can stretch a pulse, (with many peaks), out to 5ms or cook for 300 ms
if desired. And then the power flow and impedance can be adjusted for different conductivity test cells. I'm a backer of
the micropython on esp8266 and could easily use that one as a controller for this project. Are you going to commit time, and
will you license it open hardware compatible?

On 04/28/2016 03:12 PM, Nathan McCorkle wrote:
> Is electroporation preferable? From the first time I used it, my first
> summer internship, I was hooked. I thought "screw chemical
> transformation" for the, in my opinion, more elegant, tuneable,
> eco-friendly/greener-chemistry, faster, wider species coverage (you
> just vary the pulse shape/voltage, maybe the salt content of the
> buffer)... and higher efficiency to boot.
>
> Why isn't it more prominent? Because no one has made a cheaper or
> open-source version yet.

OK, so will you help me promote it with twitter, instagram, snap chat videos when the time comes?
Who to sell to besides DIYers?

There were some discussions I kept "best of" emails from before 2014 when my list server crashed
without a backup I can find anymore. We were talking with a retired Oak Ridge nuclear engineer
developing RF induction heaters using a car induction coil. It's all a little heavy and expensive compared
to the flyback parts used in laser printers -- I have a box full of those to test with...

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> It'd also be simple enough to add measurement of the discharge curve using a > voltage divider and the built in ADC of an atmega chip. > > Add an ESP8266 and you'd be able to connect via wifi+web to download and > view the conductance measurement and discharge graph for use in your > scientific article.

Telomerase gene therapy in mice extends life modestly: there are years of pretty robust results to demonstrate that. Average telomere length appears to be a reflection of aging, most likely not a significant contributer to aging. It is a poor measure, as the trend downward with age is statistical over populations. Average telomere length is some function of stem cell activity (delivering new cells with long telomeres) and cell division rates (shortening telomeres with each division). Stem cell activity declines with aging. Average telomere length is presently measured in white blood cells, which are going to have a whole lot of influences on cell division and replacement rates that don't exist in other tissues, due to immune system reactions to circumstances. Telomerase is clearly doing a lot of other things beyond telomere lengthening. Look at the work suggesting it is acting as a mitochondrial antioxidant, for example, or other cryptic activities.

The present consensus is that telomerase therapies in mice extend life through increased stem cell and/or immune activity. These telomerase therapies are clearly heading in the direction of human trials one way or another, given the results to date in mice, and the determined support of the research groups doing this. Mice have very different telomere dynamics, however, and there are concerns regarding cancer risk in humans. Trying it in dogs or primates would be the next safe thing to do - move to a mammalian species with telomere/telomerase dynamics that are closer to ours.

There is an argument that runs along these lines: telomerase gene therapy is just (primarily) another way of triggering old stem cells to get back to work, and therefore vis a vis cancer and risk should fall in the same ballpark as stem cell therapies carried out over the past fifteen years, and therefore full steam ahead because all of that work produced far less cancer that was feared. Prudence would suggest trying it out in something other than mice first, but I suspect the sudden ease of gene therapy means that this will be bypassed by the adventurous.

(I'm totally in favor of adventure when it comes to gene therapies for follistatin/myostatin - I think the risk situation there is pretty much as low as it can get prior to hundreds or thousands of enhanced human patients. I'm more cautious on the cancer and telomerase front; I think more data there would be desirable before I stepped up to try it out).

On 04/24/2016 01:39 AM, Koeng wrote: > At first glace, I am skeptical of the results. Long telomeres are > associated with some diseases. Short telomeres are associated with some > diseases. > > There is a *correlation* with telomeres and aging. From what I've read, > causation hasn't been established, meaning that lengthening telomeres most > likely won't do much. If there's any research to contradict this, my > opinion can change, but from the current papers I've read my opinion is is > that not much will happen. It'll probably do a lot of nothing. > > -Koeng > > On Friday, April 22, 2016 at 1:44:32 PM UTC, Mike Petersen wrote: >> Now this sounds interesting >> >> >> http://bioviva-science.com/2016/04/21/first-gene-therapy-successful-against-human-aging/>> >> I ask myself how exactly do they make the telomers longer and who is sure, >> there won´t be some terrible side effects? >>

Don't do that, please. People devaluing one another's work to the lowest-common-denominator is the kind of peer anti-support that keeps everyone labouring in obscurity.

Leaving asode the fact that a brick-and-mortar biohacking shop is costly (but it apparently exists!), there are significant advantages to buying a strain for the paltry cost of €30: strain identity can be known, sterility and purity guaranteed, and you're standardised with everyone else who bought that product and can avail of a community for support.

I recall getting this crap when I was planning to sell an open source plasmid *customised for DIYbio* for around €45: cheaper than pUC18 at most vendors, but I distinctly remembering someone accusing me of profiteering for not selling at $1. As if years of work designing and testing had nothing to do with making the thing and only the costs of fermentation mattered. I was even threatened that I'd be deliberately undercut and pushed out of business.

I recognize a significant difference between the IndieBB plasmid and"mycelium". It does not have any strain listed, and if someone reallywants "mycelium" they can get it for 100X cheaper, from common sourcesincluding most rotting lignocellulosic material (unlike customsynthetic engineered DNA) or for a GRAS option, a grocery store. Ididn't criticize the labelled strains they had which were apparentlycollected to achieve a wide-ranging color palette from a singlevendor.

On Thu, Apr 28, 2016 at 11:43 PM, Cathal (Phone)
<cathalgarvey@cathalgarvey.me> wrote:
> Don't do that, please. People devaluing one another's work to the
> lowest-common-denominator is the kind of peer anti-support that keeps
> everyone labouring in obscurity.
>
> Leaving asode the fact that a brick-and-mortar biohacking shop is costly
> (but it apparently exists!), there are significant advantages to buying a
> strain for the paltry cost of €30: strain identity can be known, sterility
> and purity guaranteed, and you're standardised with everyone else who bought
> that product and can avail of a community for support.
>
> I recall getting this crap when I was planning to sell an open source
> plasmid *customised for DIYbio* for around €45: cheaper than pUC18 at most
> vendors, but I distinctly remembering someone accusing me of profiteering
> for not selling at $1. As if years of work designing and testing had nothing
> to do with making the thing and only the costs of fermentation mattered. I
> was even threatened that I'd be deliberately undercut and pushed out of
> business.

I recognize a significant difference between the IndieBB plasmid and
"mycelium". It does not have any strain listed, and if someone really
wants "mycelium" they can get it for 100X cheaper, from common sources
including most rotting lignocellulosic material (unlike custom
synthetic engineered DNA) or for a GRAS option, a grocery store. I
didn't criticize the labelled strains they had which were apparently
collected to achieve a wide-ranging color palette from a single
vendor.

Don't do that, please. People devaluing one another's work to the lowest-common-denominator is the kind of peer anti-support that keeps everyone labouring in obscurity.

Leaving asode the fact that a brick-and-mortar biohacking shop is costly (but it apparently exists!), there are significant advantages to buying a strain for the paltry cost of €30: strain identity can be known, sterility and purity guaranteed, and you're standardised with everyone else who bought that product and can avail of a community for support.

I recall getting this crap when I was planning to sell an open source plasmid *customised for DIYbio* for around €45: cheaper than pUC18 at most vendors, but I distinctly remembering someone accusing me of profiteering for not selling at $1. As if years of work designing and testing had nothing to do with making the thing and only the costs of fermentation mattered. I was even threatened that I'd be deliberately undercut and pushed out of business.

I hope Petshop.bio works out and I'm confident that the prices won't be the reason it doesn't. More likely the domain name will get seized by the organic association who own .bio. ;)

This is a unique opportunity for a student that is interested in mixing biotech, creativity and retail skills! After running a number of successful concept pop-up stores at festivals and launching our online www.petshop.bio microbe store, we are now aiming to take the next step: opening up a microbe store in a busy shopping street in Amsterdam.

Customers range from DIYBiologists, curious shopping addicts to bio artists and designers. When in need if pigment producing microbes for bio ink, glowing bacteria for living lamps, mycelium for a fungi sculpture or smart slime molds to play with they turn to Petshop. There is more in our incubators, fridge and freezer that can be added too.

With Petshop.bio we aim to bring microbiology closer to the public. And Amsterdam is the perfect place for that, with multiple creative biotech spaces like our Open Wetlab and the microbe zoo Micropia. The shop is highly experimental so lots of new things to try and be prepared for the unexpected.

People from 180 nationalities live in our city, so speaking Dutch is not a prerequisite. You will become part of the Open Wetlab team at Waag Society, the home of the Dutch DIYBio community.